BBC Radio 4's World At One programme has obtained documents showing passages were removed from a National Audit Office report during consultation.
The June study was circulated to various consultees, including the government, from January. The watchdog said its main conclusions were unaltered, but others said the report was weaker than expected.
A spokesman for the National Audit Office said it was normal for reports to be passed to interested parties before publication to ensure they are "fair and accurate".
The report was published two months ago, although the NAO had produced a first draft by 26 January.
The published version said parts of the programme, aimed at linking more than 30,000 GPs to nearly 300 hospitals by 2014, were failling behind schedule and had not consulted clinicians enough.
The new systems include an online booking system, a centralised medical records system for 50m patients, e-prescriptions and fast computer network links between NHS organisations.
But the documents obtain by the BBC showed key passages had been deleted or altered.
A phrase saying the government had been "slow in securing the engagement and committment of the NHS to the programme" became more work was needed on engagement.
And a line on "insufficient trainers to train NHS staff" was taken out and instead the report said staff considered the biggest barrier to implementation was a lack of knowledge and training.
A section saying the "NHS currently lacks the sufficient skills" to deliver the programme was also deleted.
Richard Bacon, a Tory MP and member of the Public Accounts Committee, said: "I, like many, was quite surprised the NAO report because it did not reflect many of the concerns."
And Sandra Gidley, a health spokeswoman for the Liberal Democrats, said: "It is disappointing that something can be changed at the 11th hour.
"We were expecting a hard-hitting report."
But the Department of Health said while it had taken part in the consultation process its role was entirely "conventional".
A spokesman said it was up to the NAO to comment on any changes.